The 2015 merger between Kraft and Heinz created one of the largest food companies in the world. It had $28 billion in combined annual revenues and controlled dozens of food and beverage brands that for generations were staples of American households, including Heinz ketchup, Kraft cheese, Oscar Mayer meats and Planters nuts.

These days, however, the mega-merger is a mega-mess.

Sales and profits have slumped. After taking a $15.4 billion write-down in February and slashing its dividend by a third, the company reduced the value of its assets by an additional $1.22 billion last month. Securities regulators are looking into its accounting, and after an internal investigation uncovered employee misconduct, Kraft Heinz said it would restate its financials for 2016 and 2017. It faces numerous shareholder lawsuits. And after laying off thousands of people over the last four years, it announced more job cuts in the second week of August.

For the Brazilian-based investment firm 3G Capital and Warren E. Buffett’s Berkshire Hathaway, the deal has so far been a rare — and costly — misstep. While their earlier acquisitions have produced big returns, the Kraft Heinz deal has created billions of dollars in paper losses. The company’s stock has plummeted 51 percent in the past year. Last week, 3G sold more than 25 million of its Kraft Heinz shares, bringing its stake in the company down by almost 10 percent.

Some analysts and former Kraft Heinz employees place much of the blame at the feet of 3G and its use of a highly vaunted “zero-based budgeting” strategy that critics say focuses more on cutting costs than creating products that people want to buy.

Others analysts note that the company’s profit margins are much higher than at peers like General Mills and Kellogg. They argue that Kraft Heinz is facing the same headwinds as other large packaged goods companies, struggling to adapt as the public turns to healthier, and often organic, foods.

There is also competition from retailers like Walmart and Kroger, which have private-label brands. In August, Target announced plans for its own line of grocery products that it expects will include more than 2,000 items and become a multibillion-dollar brand by the end of next year.

“Kraft’s problems are in the marketplace,” said Jim Peterson, a former Kraft executive who left before the merger and is now the chief financial officer for Price Chopper Supermarkets. “Do its products have the same appeal as they used to? How are they going to grow revenues? That’s the dilemma they’re in, and it’s not easily answered.”

The person who will have to try is Miguel Patricio, who took over as chief executive in June.

“To truly change the direction of a business like ours, we need to understand the future, know where the consumer’s needs and the marketplace are headed — and then invest quickly and consistently to make sure our core brands address those needs better than our competitors,” Mr. Patricio said in an emailed statement.

Mr. Patricio declined to address questions about what happened before he arrived at the company, saying he was focusing on the “next phase of growth.”

He came to the company from Anheuser-Busch InBev, which 3G created in 2008 when it orchestrated the takeover of the American beer giant Anheuser-Busch by a company it operated called AmBev.

More acquisitions followed. In 2010, 3G acquired Burger King and took it private. In 2013, it teamed up with Mr. Buffett’s Berkshire Hathaway on a $23 billion takeover of H.J. Heinz. In 2014, the pair acquired the Canadian doughnut chain Tim Horton’s, merged it with Burger King and named the entity Restaurant Brands International.

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A Kraft Heinz booth for shareholders at Berkshire Hathaway’s annual meeting in Omaha last year.CreditDavid Williams/Bloomberg

In nearly all its deals, 3G’s strategy is fairly simple: Slash expenses, improve profitability and, typically, increase revenues by acquiring other companies. Repeat. The firm’s zero-based budgeting requires managers to justify every expense on an annual basis, not just build on the previous year’s budget. (3G did not respond to a request for comment, and Berkshire Hathaway declined to comment.)

When Kraft and Heinz merged, Bernardo Hees, a Brazilian economist who had led Burger King, became chief executive of the combined company. He told analysts that the merger would yield $1.5 billion in annual cost cuts.

Managers and employees inside Kraft said they had spent long hours and weekends after the deal closed gathering data on everything from expected travel expenses to estimates of how many paper copies their departments would make that year. Those figures were stuffed into voluminous spreadsheets and given to 3G.

That became the foundation for 3G’s cost cutting. Travel for some departments was cut in half. There were no more color printouts of presentations. Office snacks — like the free Kraft cheese and Planters nuts that employees could grab between meetings — were eliminated.

The biggest cuts came in staffing. In August 2015, about a month after the deal closed, Kraft Heinz laid off 2,500 employees, roughly 5 percent of its global work force. That included around 700 people, or about a third of the staff, at Kraft’s headquarters in Northfield, Ill. In November, Kraft Heinz announced plans to shut down seven plants in the United States and Canada, cutting 2,600 more jobs.

From London to Chicago, important responsibilities once divided among multiple employees, like market analysis and negotiations with supermarkets, fell to a single individual or a small group. With each round of layoffs, those who remained became increasingly dispirited, according to former employees. In London, talk of growing discontent at the Kraft Heinz office made it difficult to hire, said a former high-ranking official at that branch, who spoke on the condition of anonymity to discuss internal matters.

Kraft personnel, including some with decades of experience, were replaced by 3G leaders, some of whom had virtually no experience in the consumer packaged goods industry, said Robert Moskow, an analyst at Credit-Suisse who tracks Kraft Heinz.

“In other 3G companies, that strategy injected new energy and a new way of thinking and a way to get rid of sacred cows,” he said. “But it’s a very risky strategy.”

For the first year or so, it appeared the strategy was paying off. Kraft Heinz’s stock price climbed, and in early 2017 it offered to buy the European conglomerate Unilever for $143 billion. After being rebuffed, Kraft Heinz withdrew the offer a few days later.

Problems soon began to emerge. Sales started softening, and while 3G’s cost-cutting efforts resulted in robust profit margins, the stock dropped as investors got nervous.

This year, Kraft Heinz acknowledged that its problems ran deep. The company disclosed it had received a subpoena from the Securities and Exchange Commission related to an investigation of its accounting. And in February, the company took the $15.4 billion write-down, signaling that its beloved brands were less valuable than when it acquired them four years ago.

Part of the issue, analysts say, was that 3G made its cuts when Kraft Heinz should have increased research and development to compete with the start-ups increasingly taking shelf space away from food giants. In 2014, before the merger, Kraft spent $149 million on R&D. In 2017, the combined Kraft Heinz spent $93 million, according to regulatory filings.

This month, Kraft Heinz shareholders criticized the company for falling behind in the market for plant-based meat, which has drawn a surge of consumer interest and investment from major food companies.

“You’re competing now with a lot of these typically smaller start-up companies who have some version of a less processed, more natural, potentially organic product that’s more affordable and oftentimes better tasting,” said Michael Lavery, an analyst at Piper Jaffray. “It’s made it tough.”

Since the merger, some of the products that Kraft Heinz has introduced have drawn ridicule, like “salad frosting,” a repackaged ranch dressing designed to appeal to children.

Other major food manufacturers are learning from Kraft Heinz’s mistakes. General Mills has managed to improve its margins while introducing new products, like revamped macaroni and cheese recipes and a line of French-style yogurts. Mondelez, the snacks giant, has invested in smaller food start-ups.

“We’re actually in a higher cost of growth environment, where constant reinvestment is necessary,” said Mr. Moskow, the Credit Suisse analyst. “You can’t cut your way to prosperity.”